I am reading other people's code and found extensions.py in their package.
I can see the modules imported in the extensions.py are imported in init.py as well.
I could not find how the extensions.py works with init.py and in what situation you need to use the extensions.py.
Could anyone give me some explaination or provide some link that explain it?
In init.py
from flask_app.extensions import cors, guard
In extension.py
from flask_praetorian import Praetorian
cors = CORS()
guard = Praetorian()
According to Python’s package tutorial this is the minimal structure:
packaging_tutorial/
├── LICENSE
├── pyproject.toml
├── README.md
├── setup.cfg
├── src/
│ └── example_package/
│ ├── __init__.py
│ └── example.py
└── tests/
Seems as its just a backup for installing requirements, or for more readability. Maybe provide where you found extensions.py, and I can take a deeper look.
You could also dig deeper into docs and see exactly what flask-praetorian does.
I think It's just a backup for installing things like requirements.
I've been working a on a CRUD SAM application using a Python 3.8 runtime. My lambda functions reference a lambda layer that has code shared amongst the functions. My application builds/deploys and I can invoke the functions locally, however, in composing unit tests (using pytest), I'm not sure how to get around my imports referencing a layer in line that doesn't match the file structure.
File structure:
.
├── template.yaml
├── _layer-folder
│ └── _python
│ └── shared_code.py
├── _lambda
│ ├── some_function.py
│ └── _tests
│ └── test-some-function.py
When running my tests for my lambda functions, I get an import error when I reference a module in that lives in the shared layer. For example:
from some_module_in_a_layer import some_layer_function
Is there a way to configure pytest to reference the correct file directory when running the tests?
I ended up resolving this by appending to the system path when testing or running locally within my __init__.py file.
if os.environ.get("ENVIRONMENT") == "test":
sys.path.append(os.getcwd() + '/path/to/layer')
It's a pain indeed to test layers properly and it kind of depends on your method of running the test (e.g. in Pycharm or using the terminal). In PyCharm you can add the layers directory as a source (right click use as source). To run from terminal you can add it to your PYTHONPATH before running, but it's quite ugly.
So PYTHONPATH='/path/to/layer' python main.py
It's not pretty but I don't know another way to fix that tbh.
I added this line in my test and it worked perfectly.
test_file.py
import pytest
sys.path.append(os.getcwd() + '/../layer_location')
Inside layer location my file system looks like this:
layer-location\
__init__.py
layer_code.py
The import in my non-test code is then:
code_under_test.py
from layer_code import foo
foo()
In my company, we have a Python project that contains a hierarchy of lots of packages and modules shared by our different applications. But what seemed a good idea to mutualise code has become something horribly difficult to use and maintain.
Depending on the end-project, we use a single module from this library, or a single package, or many. And some modules/packages are independent, but some others depend on other packages and modules from the same library. And of course those modules depend on third-party packages.
I would like to make it as modular as possible, i.e. I would like to deal with the following cases:
use the whole library
use a single package from that library (whether it is a top level package or not)
use a single module from the library
use multiple packages/modules from the library (possibly interdependent)
Moreover, a strong constraint I have is not to break existing code so that I can make the project transformation without breaking all the projects of my coworkers...
Here is an example file tree that represents the situation:
library
├── a
│ └── i
│ ├── alpha.py # each module may depend on any other package / module
│ └── beta.py
├── b
│ ├── delta.py
│ ├── gamma.py
│ └── j
│ └── epsilon.py
├── c
│ ├── mu.py
│ └── nu.py
├── requirements.txt
└── setup.py
The best solution I found is to add a setup.py and a requirements.txt in every folder of the tree. But this has serious limitations:
I cannot use a single module (I have to use a package).
When I use a package, I have to change its import statements. For example if, before any change, I use from library.a.i import alpha, I would like not to modify it afterwards.
Moreover, I am quite sure I am forgetting some of the constraints I have...
So is what I am trying to achieve feasible, or is it utopian?
What you can do is the following:
You need to have PYTHONPATH pointing on library or append it to sys.path
eg sys.path.insert(0, 'path_to_libray')
If you create __init__.py at each level of your folders you will be able to pick whatever level/module of interest eg:
in folder b :
from .delta import *
from .gamma import *
from b.j import *
in folder j:
from .epsilon import *
You can now do in any python script:
from b import * : will import all of b contained modules
from b.j import *: will import only epsilon stuff
I used easy_install to install pytest on a Mac and started writing tests for a project with a file structure likes so:
repo/
|--app.py
|--settings.py
|--models.py
|--tests/
|--test_app.py
Run py.test while in the repo directory, and everything behaves as you would expect.
But when I try that same thing on either Linux or Windows (both have pytest 2.2.3 on them), it barks whenever it hits its first import of something from my application path. For instance, from app import some_def_in_app.
Do I need to be editing my PATH to run py.test on these systems?
I'm not sure why py.test does not add the current directory in the PYTHONPATH itself, but here's a workaround (to be executed from the root of your repository):
python -m pytest tests/
It works because Python adds the current directory in the PYTHONPATH for you.
Recommended approach for pytest>=7: use the pythonpath setting
Recently, pytest has added a new core plugin that supports sys.path modifications via the pythonpath configuration value. The solution is thus much simpler now and doesn't require any workarounds anymore:
pyproject.toml example:
[tool.pytest.ini_options]
pythonpath = [
"."
]
pytest.ini example:
[pytest]
pythonpath = .
The path entries are calculated relative to the rootdir, thus . adds repo directory to sys.path in this case.
Multiple path entries are also allowed: for a layout
repo/
├── src/
| └── lib.py
├── app.py
└── tests
├── test_app.py
└── test_lib.py
the configuration
[tool.pytest.ini_options]
pythonpath = [
".", "src",
]
or
[pytest]
pythonpath = . src
will add both app and lib modules to sys.path, so
import app
import lib
will both work.
Original answer (not recommended for recent pytest versions; use for pytest<7 only): conftest solution
The least invasive solution is adding an empty file named conftest.py in the repo/ directory:
$ touch repo/conftest.py
That's it. No need to write custom code for mangling the sys.path or remember to drag PYTHONPATH along, or placing __init__.py into dirs where it doesn't belong (using python -m pytest as suggested in Apteryx's answer is a good solution though!).
The project directory afterwards:
repo
├── conftest.py
├── app.py
├── settings.py
├── models.py
└── tests
└── test_app.py
Explanation
pytest looks for the conftest modules on test collection to gather custom hooks and fixtures, and in order to import the custom objects from them, pytest adds the parent directory of the conftest.py to the sys.path (in this case the repo directory).
Other project structures
If you have other project structure, place the conftest.py in the package root dir (the one that contains packages but is not a package itself, so does not contain an __init__.py), for example:
repo
├── conftest.py
├── spam
│ ├── __init__.py
│ ├── bacon.py
│ └── egg.py
├── eggs
│ ├── __init__.py
│ └── sausage.py
└── tests
├── test_bacon.py
└── test_egg.py
src layout
Although this approach can be used with the src layout (place conftest.py in the src dir):
repo
├── src
│ ├── conftest.py
│ ├── spam
│ │ ├── __init__.py
│ │ ├── bacon.py
│ │ └── egg.py
│ └── eggs
│ ├── __init__.py
│ └── sausage.py
└── tests
├── test_bacon.py
└── test_egg.py
beware that adding src to PYTHONPATH mitigates the meaning and benefits of the src layout! You will end up with testing the code from repository and not the installed package. If you need to do it, maybe you don't need the src dir at all.
Where to go from here
Of course, conftest modules are not just some files to help the source code discovery; it's where all the project-specific enhancements of the pytest framework and the customization of your test suite happen. pytest has a lot of information on conftest modules scattered throughout their docs; start with conftest.py: local per-directory plugins
Also, SO has an excellent question on conftest modules: In py.test, what is the use of conftest.py files?
I had the same problem. I fixed it by adding an empty __init__.py file to my tests directory.
Yes, the source folder is not in Python's path if you cd to the tests directory.
You have two choices:
Add the path manually to the test files. Something like this:
import sys, os
myPath = os.path.dirname(os.path.abspath(__file__))
sys.path.insert(0, myPath + '/../')
Run the tests with the env var PYTHONPATH=../.
Run pytest itself as a module with:
python -m pytest tests
This happens when the project hierarchy is, for example, package/src package/tests and in tests you import from src. Executing as a module will consider imports as absolute rather than relative to the execution location.
You can run with PYTHONPATH in project root
PYTHONPATH=. py.test
Or use pip install as editable import
pip install -e . # install package using setup.py in editable mode
I had the same problem in Flask.
When I added:
__init__.py
to the tests folder, the problem disappeared :)
Probably the application couldn't recognize folder tests as a module.
I created this as an answer to your question and my own confusion. I hope it helps. Pay attention to PYTHONPATH in both the py.test command line and in the tox.ini.
https://github.com/jeffmacdonald/pytest_test
Specifically: You have to tell py.test and tox where to find the modules you are including.
With py.test you can do this:
PYTHONPATH=. py.test
And with tox, add this to your tox.ini:
[testenv]
deps= -r{toxinidir}/requirements.txt
commands=py.test
setenv =
PYTHONPATH = {toxinidir}
I fixed it by removing the top-level __init__.py in the parent folder of my sources.
I started getting weird ConftestImportFailure: ImportError('No module named ... errors when I had accidentally added __init__.py file to my src directory (which was not supposed to be a Python package, just a container of all source).
It is a bit of a shame that this is an issue in Python... But just adding this environment variable is the most comfortable way, IMO:
export PYTHONPATH=$PYTHONPATH:.
You can put this line in you .zshrc or .bashrc file.
I was having the same problem when following the Flask tutorial and I found the answer on the official Pytest documentation.
It's a little shift from the way I (and I think many others) are used to do things.
You have to create a setup.py file in your project's root directory with at least the following two lines:
from setuptools import setup, find_packages
setup(name="PACKAGENAME", packages=find_packages())
where PACKAGENAME is your app's name. Then you have to install it with pip:
pip install -e .
The -e flag tells pip to install the package in editable or "develop" mode. So the next time you run pytest it should find your app in the standard PYTHONPATH.
I had a similar issue. pytest did not recognize a module installed in the environment I was working in.
I resolved it by also installing pytest into the same environment.
Also if you run pytest within your virtual environment make sure pytest module is installed within your virtual environment. Activate your virtual environment and run pip install pytest.
For me the problem was tests.py generated by Django along with tests directory. Removing tests.py solved the problem.
I got this error as I used relative imports incorrectly. In the OP example, test_app.py should import functions using e.g.
from repo.app import *
However liberally __init__.py files are scattered around the file structure, this does not work and creates the kind of ImportError seen unless the files and test files are in the same directory.
from app import *
Here's an example of what I had to do with one of my projects:
Here’s my project structure:
microbit/
microbit/activity_indicator/activity_indicator.py
microbit/tests/test_activity_indicator.py
To be able to access activity_indicator.py from test_activity_indicator.py I needed to:
start test_activity_indicatory.py with the correct relative import:
from microbit.activity_indicator.activity_indicator import *
put __init__.py files throughout the project structure:
microbit/
microbit/__init__.py
microbit/activity_indicator/__init__.py
microbit/activity_indicator/activity_indicator.py
microbit/tests/__init__.py
microbit/tests/test_activity_indicator.py
According to a post on Medium by Dirk Avery (and supported by my personal experience) if you're using a virtual environment for your project then you can't use a system-wide install of pytest; you have to install it in the virtual environment and use that install.
In particular, if you have it installed in both places then simply running the pytest command won't work because it will be using the system install. As the other answers have described, one simple solution is to run python -m pytest instead of pytest; this works because it uses the environment's version of pytest. Alternatively, you can just uninstall the system's version of pytest; after reactivating the virtual environment the pytest command should work.
I was getting this error due to something even simpler (you could even say trivial). I hadn't installed the pytest module. So a simple apt install python-pytest fixed it for me.
'pytest' would have been listed in setup.py as a test dependency. Make sure you install the test requirements as well.
Since no one has suggested it, you could also pass the path to the tests in your pytest.ini file:
[pytest]
...
testpaths = repo/tests
See documentation: https://docs.pytest.org/en/6.2.x/customize.html#pytest-ini
Side effect for Visual Studio Code: it should pick up the unit test in the UI.
We have fixed the issue by adding the following environment variable.
PYTHONPATH=${PYTHONPATH}:${PWD}/src:${PWD}/test
As pointed out by Luiz Lezcano Arialdi, the correct solution is to install your package as an editable package.
Since I am using Pipenv, I thought about adding to his answer a step-by-step how to install the current path as an edible with Pipenv, allowing to run pytest without the need of any mangling code or lose files.
You will need to have the following minimal folder structure (documentation):
package/
package/
__init__.py
module.py
tests/
module_test.py
setup.py
setup.py mostly has the following minium code (documentation):
import setuptools
setuptools.setup(name='package', # Change to your package name
packages=setuptools.find_packages())
Then you just need to run pipenv install --dev -e . and Pipenv will install the current path as an editable package (the --dev flag is optional) (documentation).
Now you should be able to run pytest without problems.
If this pytest error appears not for your own package, but for a Git-installed package in your package's requirements.txt, the solution is to switch to editable installation mode.
For example, suppose your package's requirements.txt had the following line:
git+https://github.com/foo/bar.git
You would instead replace it with the following:
-e git+https://github.com/foo/bar.git#egg=bar
If nothing works, make sure your test_module.py is listed under the correct src directory.
Sometimes it will give ModuleNotFoundError not because modules are misplaced or export PYTHONPATH="${PWD}:${PYTHONPATH}" is not working, its because test_module.py is placed into a wrong directory under the tests folder.
it should be 1-to-1 mapping relation recursively instead of the root folder should be named as "tests" and the name of the file that include test code should starts with "test_",
for example,
./nlu_service/models/transformers.py
./tests/models/test_transformers.py
This was my experience.
Very often the tests were interrupted due to module being unable to be imported.
After research, I found out that the system is looking at the file in the wrong place and we can easily overcome the problem by copying the file, containing the module, in the same folder as stated, in order to be properly imported.
Another solution proposal would be to change the declaration for the import and show MutPy the correct path of the unit. However, due to the fact that multiple units can have this dependency, meaning we need to commit changes also in their declarations, we prefer to simply move the unit to the folder.
My solution:
Create the conftest.py file in the test directory containing:
import os
import sys
sys.path.insert(0, os.path.dirname(os.path.realpath(__file__)) + "/relative/path/to/code/")
This will add the folder of interest to the Python interpreter path without modifying every test file, setting environment variable or messing with absolute/relative paths.
Setup
I have the following tree structure in my project:
Cineaste/
├── cineaste/
│ ├── __init__.py
│ ├── metadata_errors.py
│ ├── metadata.py
│ └── tests/
│ └── __init__.py
├── docs/
├── LICENSE
├── README.md
└── setup.py
metadata.py imports metadata_errors.py with the expression:
from .metadata_errors.py import *
Thus setting a relative path to the module in the same directory (notice the dot prefix).
I can run metadata.py in the PyCharm 2016 editor just fine with the following configuration:
Problem
However, with this configuration I cannot debug metadata.py. PyCharm returns the following error message (partial stack trace):
from .metadata_errors import *
SystemError: Parent module '' not loaded, cannot perform relative import
PyCharm debugger is being called like so:
/home/myself/.pyenv/versions/cineaste/bin/python /home/myself/bin/pycharm-2016.1.3/helpers/pydev/pydevd.py --multiproc --module --qt-support --client 127.0.0.1 --port 52790 --file cineaste.metadata
Question
How can I setup this project so that PyCharm is able to run and debug a file that makes relative imports?
Today (PyCharm 2018.3) it is really easy but not obvious.
You can choose target to run: script name or module name by pressing the label "Script Path" in edit configuration window:
One of possible solutions could be to run your module through intermediate script which you'll run in debug mode.
E.g. test_runner.py:
import runpy
runpy.run_module('cineaste.metadata')
You might also try removing the last node (/cineaste) from the Working Directory. This configuration works (run and debug) for me (in Pycharm: 2017.2.2)
I would suggest not using * since that can cause many problems in the future, two classes or methods being named the same etc.